That Pacific appears to have a diecast trailing truck like the one that's on the Pennsy K-5. The Chicago and Northwestern 21085 from 1958 and a few years after that had the diecast trailing truck instead of the plain/exposed wheel version like the 282 and 283 that were produced before the 1957/1958 switch to 5 digit numbers in the Flyer line. I got out a magnifying glass and it looks like a C&NW herald in the 2nd and 4th picture. There's a tuscan colored Union Pacific 3 bay hopper - that was 24216 from 1958-1960. The black lumber load flatcar is probably a 24516 NH that ran from 1957-1959, or possibly the 928 NH that ran through 1957. Yellow boxcar with tuscan roof is a MKT numbered 937 that ran until 1958 or the hyper rare 24016 from 1958 only. Single dome Gulf tankcar is either a 925 that ran through 1957 or a 24310 that was in the line from 1958-1960. Yellow generator on a depressed center Erie flatcar is either a 946 from 1957 or 24529 from 1957-1958. 3rd picture looks like a rocket launching flatcar in front of the caboose that's either a 969 from 1957 or a 25045 from 1957-1960. Caboose looks like a Reading 930 from 1953-1957 or 24603 1957-1958, 24608 from 1957, or 24610 from 1958-1960. Transformer is indeed a Lionel TW. Those are very educated guesses on the engine and cars based on what I could make out with the magnifying glass and a couple Greenberg illustrated books on Flyer.
Gilbert mixed 3 digit cars with 5 digit cars to fill out sets in 1957 and 1958; 1957 had a number of 3 digit cars appearing in the new 5 digit numbered boxes. A handful of 5 digit cars like the 24016 MKT boxcar are in the mid to high hundreds for a VG or better car. Good luck on your hunt - most of the items can be had for not too much $$$.